# FiltpostQC-EU
**Author**: Etienne Kabongo
**Affiliation**: Audrey Grant Lab – Computational Genomics, McGill University
**Contact**: [etienne@example.com](mailto:etienne@example.com)
---
## 🧬 FiltpostQC-EU: Post-GWAS Filtering Tool for Regenie Results
**FiltpostQC-EU** is a robust and lightweight Python CLI tool developed to perform post-GWAS variant-level quality control on summary statistics generated by the [REGENIE](https://rgcgithub.github.io/regenie/) software. It filters variants based on an external European QC filter file and optionally formats the results for [FUMA](https://fuma.ctglab.nl/) downstream annotation.
---
## ✨ Key Features
* ✅ **Input**: Accepts Regenie merged summary statistics.
* 📊 **Filtering**: Retains only variants present in a QC-filter file (e.g., MAF, INFO, HWE).
* 🧪 **Output**: Supports filtered `.txt` output and/or FUMA-compatible files.
* 🧠 **Bioinformatics-Ready**: Designed for UK Biobank and large-scale GWAS datasets.
* ⚙️ **CLI Interface**: Fully command-line operable with detailed help menu.
---
## 📦 Installation
```bash
pip install FiltpostQC-EU
```
Or from source:
```bash
git clone https://github.com/EtienneNtumba/FiltpostQC-EU.git
cd FiltpostQC-EU
pip install .
```
---
## 🚀 Usage
```bash
filtpostqc-eu -i path/to/regenie_merged.txt \
-f path/to/filter.tsv \
-o filtered_output.txt \
--fuma fuma_output.txt \
--format both
```
### Arguments
| Argument | Description |
| -------------- | -------------------------------------------------------------------- |
| `-i, --input` | Path to merged Regenie file (required) |
| `-f, --filter` | QC filter file (e.g., MAF/HWE/INFO based) (required) |
| `-o, --output` | Output for filtered Regenie results (default: `filtered_output.txt`) |
| `--fuma` | Output path for FUMA-formatted file (default: `fuma_output.txt`) |
| `--format` | Output format: `filtered`, `fuma`, or `both` (default: `both`) |
| `--version` | Print the tool version |
---
## 📂 Input Format
### Merged Regenie File (`P0_GWAS_qc_merged.txt`)
Must contain columns like:
```
Name Chr Pos Ref Alt Trait Effect Pval Num_Cases Num_Controls Info
```
### QC Filter File (`EUR_QC_filter_regenie.tsv`)
Must contain at least:
```
Name Chr Pos Ref Alt
```
---
## 🧬 FUMA Output Format
The FUMA-compatible file will include:
* `Chr`, `Pos`, `Name`, `Ref`, `Alt`, `Num_Cases`, `Num_Controls`, `Beta`, `Se`, `Pval`
---
## 👨🔬 About the Developer
This tool was created by **Etienne Kabongo**, computational biologist and research assistant in the **Audrey Grant Lab** at **McGill University**.
Our research focuses on large-scale genomic analyses, GWAS pipelines, and post-GWAS interpretation frameworks.
---
## 📄 License
MIT License
---
## 📬 Contact
For feedback, bug reports, or feature requests, feel free to contact:
* ✉️ Etienne Kabongo: `etienne@example.com`
---
## ⭐ Acknowledgements
* Regenie: For efficient GWAS computation
* FUMA: For functional mapping and annotation
---
> "Reliable QC is the foundation of reproducible GWAS."
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"description": "# FiltpostQC-EU\n\n**Author**: Etienne Kabongo\n**Affiliation**: Audrey Grant Lab \u2013 Computational Genomics, McGill University\n**Contact**: [etienne@example.com](mailto:etienne@example.com)\n\n---\n\n## \ud83e\uddec FiltpostQC-EU: Post-GWAS Filtering Tool for Regenie Results\n\n**FiltpostQC-EU** is a robust and lightweight Python CLI tool developed to perform post-GWAS variant-level quality control on summary statistics generated by the [REGENIE](https://rgcgithub.github.io/regenie/) software. It filters variants based on an external European QC filter file and optionally formats the results for [FUMA](https://fuma.ctglab.nl/) downstream annotation.\n\n---\n\n## \u2728 Key Features\n\n* \u2705 **Input**: Accepts Regenie merged summary statistics.\n* \ud83d\udcca **Filtering**: Retains only variants present in a QC-filter file (e.g., MAF, INFO, HWE).\n* \ud83e\uddea **Output**: Supports filtered `.txt` output and/or FUMA-compatible files.\n* \ud83e\udde0 **Bioinformatics-Ready**: Designed for UK Biobank and large-scale GWAS datasets.\n* \u2699\ufe0f **CLI Interface**: Fully command-line operable with detailed help menu.\n\n---\n\n## \ud83d\udce6 Installation\n\n```bash\npip install FiltpostQC-EU\n```\n\nOr from source:\n\n```bash\ngit clone https://github.com/EtienneNtumba/FiltpostQC-EU.git\ncd FiltpostQC-EU\npip install .\n```\n\n---\n\n## \ud83d\ude80 Usage\n\n```bash\nfiltpostqc-eu -i path/to/regenie_merged.txt \\\n -f path/to/filter.tsv \\\n -o filtered_output.txt \\\n --fuma fuma_output.txt \\\n --format both\n```\n\n### Arguments\n\n| Argument | Description |\n| -------------- | -------------------------------------------------------------------- |\n| `-i, --input` | Path to merged Regenie file (required) |\n| `-f, --filter` | QC filter file (e.g., MAF/HWE/INFO based) (required) |\n| `-o, --output` | Output for filtered Regenie results (default: `filtered_output.txt`) |\n| `--fuma` | Output path for FUMA-formatted file (default: `fuma_output.txt`) |\n| `--format` | Output format: `filtered`, `fuma`, or `both` (default: `both`) |\n| `--version` | Print the tool version |\n\n---\n\n## \ud83d\udcc2 Input Format\n\n### Merged Regenie File (`P0_GWAS_qc_merged.txt`)\n\nMust contain columns like:\n\n```\nName\tChr\tPos\tRef\tAlt\tTrait\tEffect\tPval\tNum_Cases\tNum_Controls\tInfo\n```\n\n### QC Filter File (`EUR_QC_filter_regenie.tsv`)\n\nMust contain at least:\n\n```\nName\tChr\tPos\tRef\tAlt\n```\n\n---\n\n## \ud83e\uddec FUMA Output Format\n\nThe FUMA-compatible file will include:\n\n* `Chr`, `Pos`, `Name`, `Ref`, `Alt`, `Num_Cases`, `Num_Controls`, `Beta`, `Se`, `Pval`\n\n---\n\n## \ud83d\udc68\u200d\ud83d\udd2c About the Developer\n\nThis tool was created by **Etienne Kabongo**, computational biologist and research assistant in the **Audrey Grant Lab** at **McGill University**.\n\nOur research focuses on large-scale genomic analyses, GWAS pipelines, and post-GWAS interpretation frameworks.\n\n---\n\n## \ud83d\udcc4 License\n\nMIT License\n\n---\n\n## \ud83d\udcec Contact\n\nFor feedback, bug reports, or feature requests, feel free to contact:\n\n* \u2709\ufe0f Etienne Kabongo: `etienne@example.com`\n\n---\n\n## \u2b50 Acknowledgements\n\n* Regenie: For efficient GWAS computation\n* FUMA: For functional mapping and annotation\n\n---\n\n> \"Reliable QC is the foundation of reproducible GWAS.\"\n\n",
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